droso_RS2_C4_D2_salmon.config

manifest {
   mainScript = 'main.nf'
}

params {
   reads = '/workspace/ninon/data/medium_droso/*_{1,2}.f*q.gz'
   reference_genome = '/workspace/ninon/data/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa'
   reference_cdna = '/workspace/ninon/data/Drosophila_melanogaster.BDGP6.32.cdna.all.fa'
   reference_annotation = '/workspace/ninon/data/Drosophila_melanogaster.BDGP6.32.106.gtf'
   reference_annotation_ensembl = '/workspace/ninon/data/Drosophila_melanogaster.BDGP6.32.106.gtf'
   baseDir = '/workspace/projects/Nine-s/nextflow_RS2_salmon'
   outdir = '/workspace/ninon/results'
   threads = 32
   split = 3494901
   suffix_length = 3

}

process {
   executor = 'k8s'
   scratch = true
   withName:CHECK_STRANDNESS {
      container = 'ninedem/check_strandedness:latest'
   }

   withLabel:fastp {
      container = 'biocontainers/fastp:v0.20.1_cv1'
   }
   withLabel:python {
      container = 'phips/pandas:v3'
   }
   withLabel:salmon {
      container = 'combinelab/salmon:1.7.0'
   }
   withLabel:bash {
      container = 'nfcore/rnaseq:1.4.2'
}
   withLabel:samtools {
      container = 'biocontainers/samtools:v1.7.0_cv4'
   }
   withName:split_fastq { 
      container = 'nfcore/rnaseq:1.4.2'
   }
}
docker {
   enabled = true
}

k8s {
   debug {
      yaml = true
   }
   namespace = 'default'
   context = 'bountrisv-hu'
   runAsUser = 0
   storageClaimName = 'nextflow-ninon'
   storageMountPath = '/workspace'
}

trace {
   enabled = true
   file = '_trace_RS2_C4_D2_salmon'
   fields = 'task_id, hash, native_id, process, tag, name, status, exit, module, container, cpus, time, disk, memory, attempt, submit, start, complete, duration, realtime, queue, %cpu, %mem, rss, vmem, peak_rss, peak_vmem, rchar, wchar, syscr, syscw, read_bytes, write_bytes, vol_ctxt, inv_ctxt, env, workdir, script, scratch, error_action'
}

report {
   enabled = true
   file = '_report_RS2_C4_D2_salmon.html'
}

timeline {
   enabled = true
   file = '_timeline_RS2_C4_D2_salmon'
}

dag {
   enabled = true
   file = '_dag_RS2_C4_D2_salmon'
}